That's a very deep question. All I know is that I researched it on-line and found three Christian web sites devoted to the subject of Satanic flies, conversations on twitter about it, and five Bible quotes mentioning flies as being a sign of the Devil. It's so much a part of our culture, flies were used in the Hollywood movie "The Omen" to portray the presence of Satan.
Apparently other insects are identified in the Bible as portents of evil as well. Locusts and bees for instance. Frogs are similarly vilified as being "unclean creatures" associated with demons, (Revelation 16:13). I don't know why the Devil would be inclined to use one animal over another to torment mankind, but there is plenty of biblical evidence he favors certain beasts like the "jackal" for instance, which receives numerous mentions in the Old Testament as a portent of war and coming destruction. The "jackal" was featured in the Exorcist sequels, (substituted for the much more fierce looking hyena for dramatic effect). Because of their history of service in Roman Legions as attack dogs, In the Omen movies, Rottweiler dogs were portrayed as minions of the Devil. Black cats are also associated with witchcraft according to superstition, but I don't think there is any direct biblical evidence that Rottweilers or black cats are evil.
I don't think God can be held personally responsible for how Lucifer or fallen angels (demons) use the animal kingdom to accomplish injury to humans, or mankind himself for that matter. This is a general theology question better suited to that particular forum.
I hope everyone has enjoyed this brief intermission from all the political vitriol, nevertheless, a Satanic fly did land on Hillary Clinton's forehead at the beginning of the last presidential debate. Lol.